Pavano (8-6) won his third straight start while snapping a three-game road losing streak. The right-hander struck out two and walked none in his ninth career complete game.
"The ground balls were all gobbled up," Pavano said. "The boys played great behind me and we beat a tough pitcher today."
"Pavano was fantastic," Twins manager Ron Gardenhire said. "That's an unbelievable lineup they have over there, but he kept them off balance and got his pitches over for strikes."
Jason Kubel and Joe Mauer had RBI singles for the AL Central leaders, who pounded out 11 hits off Halladay and took the final two games of the three-game series. Minnesota rallied from a five-run deficit in the ninth inning Saturday and won in the 11th.
Halladay (8-6) lost his third straight start, giving up a season high in hits while striking out eight and walking none in eight innings. In his last two starts, the right-hander has yielded 10 runs (nine earned) and 19 hits, including five homers, in 14 innings.
"I pitched to contact and they put the ball in play and sometimes found holes," Halladay said. "The two homers are what really cost me."
Halladay didn't get much help from his offense, which appeared to be snapping out of its funk by scoring 32 runs in its last four games after averaging 2.4 runs during a 6-15 stretch. Besides Valdez's homer and Howard's hit, the Phillies got only a pair of fourth-inning singles by Placido Polanco and Chase Utley.
"We didn't put up enough offense to win," manager Charlie Manuel said. "Pavano held us down. He was moving the ball around, using all of his pitches. We hit some balls hard early, but they got caught."
Philadelphia has totaled nine runs in Halladay's six losses.
"My job is to focus on executing pitches whether we score nine or none," Halladay said.
Mauer's RBI single in the first inning scored Orlando Hudson. The Twins extended the advantage to two runs with Span's one-out homer in the fifth.
Valdez pulled the Phillies within 2-1 in the bottom half by hitting a home run to left for the second straight day. It marked a surprising power surge for Valdez, who homered once in his first 451 major league at-bats before connecting twice in his next six.
Minnesota, however, got the run back in the sixth when Morneau scored on Kubel's single to right.
Morneau reached second in strange fashion. He singled to center, took a big turn around first and raced to second when Shane Victorino threw behind him trying to get him out at first. Victorino was charged with an error on the play.
Kubel went 2 for 4, extending his hitting streak to 12 games while finally solving Halladay. Kubel entered 1 for 17 against the ace right-hander.
Morneau's solo homer to right in the eighth made it 4-1.
Minnesota OF Delmon Young has hit safely in 15 of 16 games after going 1 for 4 with a second-inning double. ... Pavano's second-inning single was his first hit since 2004 with Florida. He had been hitless in his last nine at-bats. ... Minnesota, which made its first trip to Citizens Bank Park, improved to 139-101 in interleague play.